This change looks simple but Anjuta needs to parse the configure.ac file
and rewrite which is something tricky. I suppose it isn't done correctly
in your case. Could you open a bug report and attach your configure.ac
file, so I can check this?

Sorry for the delay. Will do that if necessary, but I noticed the motive
is that the version in configure.in is between [ ]. The newer versions
are saved behind the brackets, but the brackets are not erased. Like
this:
AC_INIT([lbl_server], [1.01])
AC_INIT([lbl_server], [1.01]1.02)
AC_INIT([lbl_server], [1.01]1.021.03)
Maybe the brackets confuse the parser?
John